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http://bioconductor.org/packages/GenomicFeatures/

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

Proper citation: GenomicFeatures (RRID:SCR_016960) Copy   

•   Source: SciCrunch Registry

https://omicssimla.sourceforge.io

Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.

Proper citation: OmicsSIMLA (RRID:SCR_017011) Copy   

•   Source: SciCrunch Registry

https://www.iigm.it/site/index.php?l=ENG

Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.

Proper citation: Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicRanges/

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

Proper citation: Genomic Ranges (RRID:SCR_017051) Copy   

•   Source: SciCrunch Registry

http://www.cisreg.ca/cgi-bin/NHR-scan/nhr_scan.cgi

Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications.

Proper citation: Nuclear Hormone Receptor Scan (RRID:SCR_016975) Copy   

•   Source: SciCrunch Registry

https://www.a-star.edu.sg/gis/Our-Science/Technology-Platforms/Scientific-and-Research-Computing

Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers.

Proper citation: Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) Copy   

•   Source: SciCrunch Registry

https://ircm.qc.ca/en/technological-services/bioinformatics

Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses.

Proper citation: Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) Copy   

•   Source: SciCrunch Registry

https://github.com/hillerlab/GenomeAlignmentTools

Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences.

Proper citation: RepeatFiller (RRID:SCR_017414) Copy   

•   Source: SciCrunch Registry

https://arxiv.org/abs/1308.2012

Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.

Proper citation: GCE (RRID:SCR_017332) Copy   

•   Source: SciCrunch Registry

https://4dgenome.research.chop.edu/

Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community.

Proper citation: 4D Genome (RRID:SCR_017489) Copy   

•   Source: SciCrunch Registry

https://amoebadb.org/amoeba/

Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.

Proper citation: AmoebaDB (RRID:SCR_017592) Copy   

•   Source: SciCrunch Registry

http://www.mogene.com/

Core provides services to its partners in deploying genomic capabilities to bring critical solutions to both agriculture and industrial biotech operations. Core facility also provides assistance to research, biotech/pharma and government facilities. In addition to being an Agilent Certified Service Provider MOgene is also a CLIA certified genomics service facility offering one stop service and solution from Tissue/Cells to Analysis. Core offers RNA/DNA isolation, Microarrays, NextGen sequencing, Real time PCR and bioinformatics services.

Proper citation: MOgene (RRID:SCR_012433) Copy   

•   Source: SciCrunch Registry

http://sift.bii.a-star.edu.sg/

Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.

Proper citation: SIFT (RRID:SCR_012813) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

Proper citation: Blixem (RRID:SCR_015994) Copy   

•   Source: SciCrunch Registry

http://starbase.sysu.edu.cn/index.php

Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.

Proper citation: Starbase V2.0 (RRID:SCR_016303) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.mdc-berlin.de/pigx/

Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data.

Proper citation: PiGx (RRID:SCR_016476) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/gatk/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.

Proper citation: IndelGenotyper (RRID:SCR_016663) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

Proper citation: Entrez (RRID:SCR_016640) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/GRO

Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of).

Proper citation: Gene Regulation Ontology (RRID:SCR_010590) Copy   

•   Source: SciCrunch Registry

http://www.crg.eu

International biomedical research institute created in December 2000 to discover and advance knowledge for benefit of society, public health and economic prosperity. Non profit foundation. Group leaders are recruited internationally and receive support from centre to set up and run their groups. External Scientific Advisory Board, made up of 15 world leaders in different areas, evaluates them.

Proper citation: Centre for Genomic Regulation; Barcelona; Spain (RRID:SCR_011147) Copy   

•   Source: SciCrunch Registry